OK, Debian 4.0 is way outdated, but I think for such a special-purpose-machine it doesn't matter. The point is that a 2.4-kernel can support USB, but since you are using a realtime-kernel (I would assume compiled by your vendor) it may be that the usb-storage support is not enabled.
I think it would really be the best to ask your vendor. There may be drivers be compiled into your kernel, or as a module, that are not part of a standard kernel (which is also not realtime), so exchanging the kernel is a no-go without asking the support before.

Thank you for your support, I plan to address this issue with my vendor.
Because we where able to confirm my inital suspicion (that the kernel is the issue), I will consider the issue as solved.